Job ID = 6367853 SRX = SRX4085421 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:38:44 prefetch.2.10.7: 1) Downloading 'SRR7167450'... 2020-06-15T23:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:00 prefetch.2.10.7: 1) 'SRR7167450' was downloaded successfully Read 17365888 spots for SRR7167450/SRR7167450.sra Written 17365888 spots for SRR7167450/SRR7167450.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:30 17365888 reads; of these: 17365888 (100.00%) were paired; of these: 9090614 (52.35%) aligned concordantly 0 times 6995124 (40.28%) aligned concordantly exactly 1 time 1280150 (7.37%) aligned concordantly >1 times ---- 9090614 pairs aligned concordantly 0 times; of these: 406013 (4.47%) aligned discordantly 1 time ---- 8684601 pairs aligned 0 times concordantly or discordantly; of these: 17369202 mates make up the pairs; of these: 12512038 (72.04%) aligned 0 times 4301038 (24.76%) aligned exactly 1 time 556126 (3.20%) aligned >1 times 63.98% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 699218 / 8533617 = 0.0819 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:05:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:30: 1000000 INFO @ Tue, 16 Jun 2020 09:05:35: 2000000 INFO @ Tue, 16 Jun 2020 09:05:41: 3000000 INFO @ Tue, 16 Jun 2020 09:05:46: 4000000 INFO @ Tue, 16 Jun 2020 09:05:52: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:05:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:58: 6000000 INFO @ Tue, 16 Jun 2020 09:06:01: 1000000 INFO @ Tue, 16 Jun 2020 09:06:05: 7000000 INFO @ Tue, 16 Jun 2020 09:06:08: 2000000 INFO @ Tue, 16 Jun 2020 09:06:12: 8000000 INFO @ Tue, 16 Jun 2020 09:06:16: 3000000 INFO @ Tue, 16 Jun 2020 09:06:19: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:06:23: 4000000 INFO @ Tue, 16 Jun 2020 09:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:06:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:26: 10000000 INFO @ Tue, 16 Jun 2020 09:06:30: 5000000 INFO @ Tue, 16 Jun 2020 09:06:31: 1000000 INFO @ Tue, 16 Jun 2020 09:06:33: 11000000 INFO @ Tue, 16 Jun 2020 09:06:38: 6000000 INFO @ Tue, 16 Jun 2020 09:06:39: 2000000 INFO @ Tue, 16 Jun 2020 09:06:40: 12000000 INFO @ Tue, 16 Jun 2020 09:06:46: 7000000 INFO @ Tue, 16 Jun 2020 09:06:47: 13000000 INFO @ Tue, 16 Jun 2020 09:06:48: 3000000 INFO @ Tue, 16 Jun 2020 09:06:54: 14000000 INFO @ Tue, 16 Jun 2020 09:06:54: 8000000 INFO @ Tue, 16 Jun 2020 09:06:56: 4000000 INFO @ Tue, 16 Jun 2020 09:07:01: 15000000 INFO @ Tue, 16 Jun 2020 09:07:02: 9000000 INFO @ Tue, 16 Jun 2020 09:07:04: 5000000 INFO @ Tue, 16 Jun 2020 09:07:08: 16000000 INFO @ Tue, 16 Jun 2020 09:07:10: 10000000 INFO @ Tue, 16 Jun 2020 09:07:12: 6000000 INFO @ Tue, 16 Jun 2020 09:07:15: 17000000 INFO @ Tue, 16 Jun 2020 09:07:18: 11000000 INFO @ Tue, 16 Jun 2020 09:07:20: 7000000 INFO @ Tue, 16 Jun 2020 09:07:22: 18000000 INFO @ Tue, 16 Jun 2020 09:07:26: 12000000 INFO @ Tue, 16 Jun 2020 09:07:28: 8000000 INFO @ Tue, 16 Jun 2020 09:07:29: 19000000 INFO @ Tue, 16 Jun 2020 09:07:33: 13000000 INFO @ Tue, 16 Jun 2020 09:07:35: 9000000 INFO @ Tue, 16 Jun 2020 09:07:36: 20000000 INFO @ Tue, 16 Jun 2020 09:07:41: 14000000 INFO @ Tue, 16 Jun 2020 09:07:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:41: #1 total tags in treatment: 7595661 INFO @ Tue, 16 Jun 2020 09:07:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:07:41: #1 tags after filtering in treatment: 6587443 INFO @ Tue, 16 Jun 2020 09:07:41: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:07:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:42: #2 number of paired peaks: 534 WARNING @ Tue, 16 Jun 2020 09:07:42: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:42: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:07:42: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05_model.r WARNING @ Tue, 16 Jun 2020 09:07:42: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:42: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:07:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:07:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:43: 10000000 INFO @ Tue, 16 Jun 2020 09:07:49: 15000000 INFO @ Tue, 16 Jun 2020 09:07:51: 11000000 INFO @ Tue, 16 Jun 2020 09:07:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:57: 16000000 INFO @ Tue, 16 Jun 2020 09:07:59: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.05_summits.bed INFO @ Tue, 16 Jun 2020 09:08:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3629 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:04: 17000000 INFO @ Tue, 16 Jun 2020 09:08:07: 13000000 INFO @ Tue, 16 Jun 2020 09:08:12: 18000000 INFO @ Tue, 16 Jun 2020 09:08:15: 14000000 INFO @ Tue, 16 Jun 2020 09:08:19: 19000000 INFO @ Tue, 16 Jun 2020 09:08:23: 15000000 INFO @ Tue, 16 Jun 2020 09:08:27: 20000000 INFO @ Tue, 16 Jun 2020 09:08:30: 16000000 INFO @ Tue, 16 Jun 2020 09:08:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:32: #1 total tags in treatment: 7595661 INFO @ Tue, 16 Jun 2020 09:08:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:08:32: #1 tags after filtering in treatment: 6587443 INFO @ Tue, 16 Jun 2020 09:08:32: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:08:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:33: #2 number of paired peaks: 534 WARNING @ Tue, 16 Jun 2020 09:08:33: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:33: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:08:33: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:08:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10_model.r WARNING @ Tue, 16 Jun 2020 09:08:33: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:33: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:08:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:08:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:38: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:45: 18000000 INFO @ Tue, 16 Jun 2020 09:08:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:52: 19000000 INFO @ Tue, 16 Jun 2020 09:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2038 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:58: 20000000 INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:09:03: #1 total tags in treatment: 7595661 INFO @ Tue, 16 Jun 2020 09:09:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:09:04: #1 tags after filtering in treatment: 6587443 INFO @ Tue, 16 Jun 2020 09:09:04: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:09:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:04: #2 number of paired peaks: 534 WARNING @ Tue, 16 Jun 2020 09:09:04: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:04: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:09:04: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:04: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:04: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:09:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:09:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085421/SRX4085421.20_summits.bed INFO @ Tue, 16 Jun 2020 09:09:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (915 records, 4 fields): 2 millis CompletedMACS2peakCalling